J-M-Dundee
commented
5 months ago I got the pipeline to run! Looks like I needed to manually select the plugins directory with:
--plugins-directory=/PATH/TO/Cellprofiler-Plugins
However now it is not producing output files even though I am specifying an output file location with:
-o /PATH/TO/Output/
Any ideas about how to fix this?
Hi there! I am trying to analyse images using cellprofiler with the runcellpose module in a python 3.8 virtual environment on an HPC. I have managed to install cellprofiler and cellpose onto my virtual environment and copied across the updated plugin .py files from the depository however it does not appear to recognise that runcellpose.py is in the plugins folder. I have also made sure to download all the dependencies but still receive the error:
ValueError: Could not find the RunCellpose moduleWould really appreciate if anyone has an idea where to go from here! Here is a copy of my pip freeze:
absl-py==2.1.0 annotated-types==0.6.0 astunparse==1.6.3 boto3==1.34.79 botocore==1.34.79 cachetools==5.3.3 cellpose==3.0.7 CellProfiler==4.2.6 cellprofiler-core==4.2.6 centrosome==1.2.2 certifi==2024.2.2 charset-normalizer==3.3.2 contourpy==1.1.1 csbdeep==0.7.4 cycler==0.12.1 deprecation==2.1.0 docker==7.0.0 docutils==0.15.2 edt==2.4.0 fastremap==1.14.1 filelock==3.13.3 flatbuffers==24.3.25 fonttools==4.51.0 fsspec==2024.3.1 future==1.0.0 gast==0.4.0 google-auth==2.29.0 google-auth-oauthlib==1.0.0 google-pasta==0.2.0 grpcio==1.62.1 h5py==3.6.0 idna==3.6 igraph==0.11.4 imagecodecs==2023.3.16 imageio==2.34.0 imglyb==2.1.0 importlib_metadata==7.1.0 importlib_resources==6.4.0 inflect==6.2.0 javabridge==1.0.19 jgo==1.0.5 Jinja2==3.1.3 jmespath==1.0.1 joblib==1.4.0 JPype1==1.5.0 keras==2.13.1 kiwisolver==1.4.5 labeling==0.1.13 libclang==18.1.1 llvmlite==0.41.1 mahotas==1.4.14 Markdown==3.6 MarkupSafe==2.1.5 matplotlib==3.7.5 mgen==1.2.1 mpmath==1.3.0 mysqlclient==1.4.6 natsort==8.4.0 ncolor==1.2.1 networkx==3.1 numba==0.58.1 numpy==1.24.3 nvidia-cublas-cu12==12.1.3.1 nvidia-cuda-cupti-cu12==12.1.105 nvidia-cuda-nvrtc-cu12==12.1.105 nvidia-cuda-runtime-cu12==12.1.105 nvidia-cudnn-cu12==8.9.2.26 nvidia-cufft-cu12==11.0.2.54 nvidia-curand-cu12==10.3.2.106 nvidia-cusolver-cu12==11.4.5.107 nvidia-cusparse-cu12==12.1.0.106 nvidia-nccl-cu12==2.19.3 nvidia-nvjitlink-cu12==12.4.127 nvidia-nvtx-cu12==12.1.105 oauthlib==3.2.2 omnipose==1.0.6 opencv-python-headless==4.9.0.80 opt-einsum==3.3.0 packaging==24.0 pandas==2.0.3 pbr==6.0.0 peakdetect==1.2 Pillow==9.5.0 prokaryote==2.4.4 protobuf==4.25.3 psutil==5.9.8 pyasn1==0.6.0 pyasn1_modules==0.4.0 pydantic==2.6.4 pydantic_core==2.16.3 pyimagej==1.4.1 pyparsing==3.1.2 python-bioformats==4.0.7 python-dateutil==2.9.0.post0 python-javabridge==4.0.3 pytz==2024.1 PyWavelets==1.4.1 PyYAML==6.0.1 pyzmq==22.3.0 requests==2.31.0 requests-oauthlib==2.0.0 roifile==2023.5.12 rsa==4.9 s3transfer==0.10.1 scikit-image==0.18.3 scikit-learn==0.24.2 scipy==1.9.0 scyjava==1.9.1 sentry-sdk==0.18.0 six==1.16.0 stardist==0.8.5 sympy==1.12 tensorboard==2.13.0 tensorboard-data-server==0.7.2 tensorflow==2.13.1 tensorflow-estimator==2.13.0 tensorflow-io-gcs-filesystem==0.34.0 termcolor==2.4.0 texttable==1.7.0 threadpoolctl==3.4.0 tifffile==2022.4.8 torch==2.2.2 torchvf==0.1.4 torchvision==0.17.2 tqdm==4.66.2 triton==2.2.0 typing_extensions==4.11.0 tzdata==2024.1 urllib3==1.26.18 Werkzeug==3.0.2 wrapt==1.16.0 wxPython==4.1.0 xarray==2023.1.0 zipp==3.18.1